Fighting drug-resistant microbes

AMR (Antimicrobial resistance) presents a serious threat to global health systems, food production and the environment. It is a peril of our own making – overuse of antimicrobial drugs is making them increasingly ineffective at treating infections and preventing the spread of disease.

The Global Research on Antimicrobial Resistance (GRAM) study published in January 2022 estimated that almost 5M deaths were associated with AMR, with 1.3M deaths in 2019 being directly attributable to AMR. Bacterial infections resulted in one in eight deaths globally in 2019 – estimated at 7.7M. The highest rates were found in Sub-Saharan Africa and South Asia. These countries are particularly exposed to the AMR threat because they have a higher number of cases of infectious diseases and fewer healthcare resources.

Human ingenuity and a coordinated global effort are needed to control this threat.

Our client, the UK Department of Health and Social Care, has placed the Fleming Fund at the centre of the UK’s global effort to tackle AMR. It provides targeted investment across selected low- and middle-income countries in Africa and Asia to help strengthen national, regional, and global surveillance systems for monitoring AMR, and encouraging the use of this data to inform effective policymaking. 

We have designed and managed a portfolio of regional and country grants to strengthen AMR surveillance systems in 22 countries. Our local presence and global reach, coupled with technical and programme management expertise enabled us to set up the Fleming Fund across Africa and Asia, effectively addressing technical and policy challenges in each country.

AMR is a cross-cutting issue and aligns with the work Mott MacDonald was already doing across many of its practices that contribute to the UN’s Sustainable Development Goals. For example, our work to improve water and sanitation, urban infrastructure design and waste management is integral to combating AMR by reducing exposure to drug resistant microbes. This shows how a multi-disciplinary approach is necessary to tackle AMR, while also helping to improve social and environmental outcomes.

The programme entered its second phase at the start of this year and runs until March 2026.

A broad strategy

The success of the programme depends on the quality and quantity of data that flows from each country’s laboratories into national and global surveillance systems. We work with governments to identify and fill gaps in national AMR capacity, ensuring that funding is distributed where it can achieve most value and in countries with the highest vulnerabilities.

The Fleming Fund’s grants have enabled governments with overstretched health budgets to strengthen laboratory and diagnostic capacity at 240 sites and improve biosafety and biosecurity to ensure bacterial samples are collected, handled, processed, and stored safely.

Taking a multidisciplinary One Health approach to combating AMR is an integral part of the programme. Some drug-resistant viruses, bacteria, fungi, and parasites move freely between humans, animals, and the environment; therefore, they cannot be effectively controlled without cross-sectoral collaboration.

Advanced equipment

Advanced lab equipment, including bacterial culture and antimicrobial susceptibility testing instruments and mass spectrometers, has been delivered to human and animal health laboratories to improve AMR testing accuracy and increase AMR testing capacity. Funding has also been used to upgrade information management and quality assurance systems and provide training to ensure data is collected, monitored, interpreted and shared effectively.

The Fleming Fund also has a fellowship programme, which has created a global network of multidisciplinary AMR experts and advocates. We have supported 184 fellows across 22 countries, providing peer-to-peer mentoring and training. These experts are forging strong links across the human, animal, and environmental health sectors, sharing knowledge, furthering collaboration, and pushing for greater alignment in policy and strategy.

Equipping laboratories and creating a global network of experts

Building sustainable capacity

Well-resourced bacteriology laboratories are in short supply in low- and middle-income countries. Historically, funding from international donors towards laboratory strengthening has focused on other public health concerns including tuberculosis, HIV, and malaria. When the Fleming Fund launched, few hospital laboratories had the equipment or capacity to conduct good quality, safe diagnoses, and surveillance of drug resistant bacteria.

As the management agent our starting point was to ensure that investment in each country was underpinned by a clear national strategy for AMR. Before each country received its first tranche of funding, we worked with its government to understand the nuances and complexities of the systems we were seeking to support. In some cases, this inception phase took six to eight months – but it was critical for the programme’s success, ensuring that investments were part of a wider strategy to deliver high quality outcomes.

We worked with national AMR co-ordination committees of health practitioners to provide technical advice on what data should be collected and which laboratories were suitable as AMR surveillance sites. Together, we determined how data would flow to a national reference laboratory to be analysed, and how it would link into the Global AMR Surveillance System (GLASS), which tracks AMR data on humans and is managed by the World Health Organization (WHO).

Improving data sharing

Countries were also supported to improve co-ordination and data sharing between government departments to facilitate a cross-sectoral approach. This groundwork allowed us to eliminate the risk that grants would fund improvements in bacteriology surveillance without taking a holistic approach to the AMR problem.

“We carefully planned our country grants to get the best value and to ensure that foundational issues were addressed by governments before providing funds,” says Dr Vikas Aggarwal, our regional director for the Fleming Fund in Asia.

“We also focused on aligning the Fleming Fund with the governments’ own investment plans – this reduced the risk of money being invested in an area where it could not be sustained. We can provide technical training or equipment, but not if the government has no resources to support a technician in the lab.” 

As part of our work with the Fleming Fund, we are also working with the UN’s Food & Agriculture Organization (FAO) and the World Organisation for Animal Health (WOAH) to promote alignment with international standards. We will also be including the UN Environment Programme (UNEP) to ensure progress in establishing environmental surveillance systems for AMR.

Systems in the veterinary, food and environment sectors are generally at an earlier stage of development or implementation than their counterparts in the human health sector, because these sectors have previously received little investment. By working across all sectors, we ensure a coordinated and effective response to AMR.

Nurturing expertise and connections

Alongside the numerous technical challenges in tackling AMR, there are a huge range of policy implications that cut across the One Health sectors – human, animal, and the environment. The Fleming Fund fellowships support the professional development of AMR practitioners and influencers. We partner with universities and other institutions across the world to provide high quality mentorship and training.

In Kenya, the programme has sparked collaboration and friendship between two policy fellows – Dr Evelyn Wesangula, patient safety unit lead at the Ministry of Health in Kenya with over 15 years’ experience as a pharmacist, and Dr Romona Ndanyi, head of Kenya’s National Veterinary reference laboratory for AMR in animal health as a veterinarian for more than 20 years.

The duo say they benefited from compassionate leadership training, communication tutorials, mentoring and lectures on policy issues provided by the University of Edinburgh. “Policy discussions with members of the Scottish government were a useful way to learn about how human and animal health staff in Scotland work together to deal with AMR challenges that we also face in Kenya,” says Dr Ndanyi.

Coaching and mentoring have helped them to work more effectively in multisector AMR teams with colleagues across the Ministries for Health, Agriculture and the Environment, with the ministries now sharing resources and collaborating more closely. The pair have also built open communication through an active WhatsApp group with members from each ministry.

“We are equal players with equal responsibility when we plan and chair AMR meetings, and we speak with one voice on AMR issues,” says Dr Wesangula, who is also a senior AMR Project Officer at the WHO, supporting east, central and southern African countries to implement NAPs on AMR. “We all own the problem and the actions, which makes a big difference when it comes to implementing interventions.”

Thanks to Fleming Fund support, AMR data on humans, animals and the environment is now available in Kenya. The data findings have encouraged the various sectors to act on AMR. “If there wasn’t national data available then people might say, ‘this is not an issue in our sector’ or ‘this is being driven externally’,” says Dr Wesangula.

Instead, each sector can see that they have a part to play in bringing solutions to the table. “Solutions are not one-sided; they come from multiple sources,” says Dr Wesangula. “That is the best thing that can happen in any multisectoral team.”

Visit to Uganda’s National mycobacterium reference laboratory

Direct clinical benefits

One priority for Fleming Fund phase II is to increase the production of high quality, robust data to inform effective policymaking. This includes changing clinical practice to improve antimicrobial prescribing. This will also be extended to pharmacists, veterinarians, and other practitioners to improve antimicrobial use in each country.

We are working with our partners to drive improvements in the quality and speed of bacteriology testing. The rollout of cutting-edge laboratory platforms for bacterial identification and antimicrobial susceptibility testing is accelerating change. For example, the VITEK 2 Compact platform can deliver AMR test results in five to eight hours, compared with 48 hours for conventional, manual methods – significantly speeding up the time taken to return these to doctors.  

There is also early evidence of AMR data being used successfully to inform clinical decisions. For example, a blood culture service at the national hospital of Timor-Leste has dramatically changed the treatment of babies with severe neonatal sepsis. Clinicians can now use a targeted antibiotic therapy which is effective even against multi-drug-resistant bacterial bloodstream infections, giving these babies a better chance of recovery.

These positive interventions will help demonstrate to clinicians and patients that there is value in blood tests. This will be critical to ensure the long-term sustainability of the programme, helping to curtail rising AMR rates in the future.

“If clinicians start to use and value information about bacterial resistance when treating patients, then they will advocate for it to be continued,” says Dr Catriona Waddington, an economist who chairs the expert advisory group that advises on our work for the Fleming Fund. “Pressure from clinicians plays an important role in securing sustained funding for AMR testing from governments.”

Improving the quality and speed of bacteriology testing

Beyond the programme

National and international policymakers require information to monitor and control infections and to prepare for future health, environmental and economic impacts. Global AMR surveillance supports more informed decision-making, but it requires ongoing funding.

We are investigating the economics of AMR data collection in countries with a variety of laboratory setups and seeking sustainable ways for them to continue AMR testing without external support.

The success of the first phase of the programme has already convinced some governments to cover the cost of certain items in their budgets. For example, the government of Timor-Leste has agreed to pay an increasing proportion of the running costs of doing the tests.

“We are working with local stakeholders to demonstrate how hospitals can be linked together in a national surveillance system, feeding in information about who is getting infected, where and with what. When coupled with information on antimicrobial use and data from agriculture, this provides decisionmakers with a huge amount of intelligence about drug resistance,” says Dr Toby Leslie, global technical lead for the Fleming Fund and a health specialist in epidemiology.

AMR awareness

AMR is a complex and evolving problem with implications across a diverse range of policy areas. Rising urbanisation, a global trend, is affecting disease transmission not just directly but also through how we process waste, where we get our food and how it is produced. These factors can heighten the AMR threat.

To mitigate risks more effectively, better communication is needed between experts, policymakers, and the public about the dangers AMR poses to human, animal and environmental health.

Fleming Fund fellow Dr Evelyn Wesangula, with a background in pharmacy, and Dr Romona Ndanyi, an animal health expert, have worked together to produce a documentary called ‘The Silent Pandemic’ to improve AMR understanding in Kenya. It launched successfully in November 2022 during Kenya’s national AMR awareness day event.

The Fleming Fund’s fellowship scheme, managed by Mott MacDonald, funded communication tutorials with academics at the University of Edinburgh, which encouraged the duo to work on the documentary as a new way to raise awareness about AMR across the Kenyan government. “The communication tutorials during the fellowship gave us advice on how to tell our story; how to identify our audience and create messages targeted at them,” says Dr Ndanyi.

The documentary includes people with a variety of informed perspectives including those with life experience of AMR, infectious disease doctors and representatives from the ministries of health, agriculture, and the environment. One of the aims was to encourage support for the country’s AMR national action plan across Kenya’s devolved system of government, particularly at county level.

“We knew we needed to communicate in a different way. For five years, we had been speaking about AMR in a technical way and not getting the kind of support that we hoped for. We thought that communicating in a different way would speak to more people and get the message home,” says Dr Wesangula.